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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of human normal blood cell subtypes

ABSTRACT: We used antibodies coupled to magnetic beads (MACS) to purify cell types out of whole blood from healthy donors (CD4+ T cells, CD8+ T cells, and B cells). We also profiled whole blood (collected in Pax tubes) and Peripheral Blood Mononuclear cells obtained by Ficoll-Paque based separation. RNA was extracted using Trizol, amplified linearly twice, labeled with Cy5 and co-hybridized with amplified Stratagene human reference (labeled with Cy3).

ORGANISM(S): Homo sapiens

SUBMITTER: Janos Demeter

PROVIDER: E-SMDB-3696 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Cell-type specific gene expression profiles of leukocytes in human peripheral blood.

Palmer Chana C Diehn Maximilian M Alizadeh Ash A AA Brown Patrick O PO

BMC genomics 20060516

<h4>Background</h4>Blood is a complex tissue comprising numerous cell types with distinct functions and corresponding gene expression profiles. We attempted to define the cell type specific gene expression patterns for the major constituent cells of blood, including B-cells, CD4+ T-cells, CD8+ T-cells, lymphocytes and granulocytes. We did this by comparing the global gene expression profiles of purified B-cells, CD4+ T-cells, CD8+ T-cells, granulocytes, and lymphocytes using cDNA microarrays.<h4 ...[more]

PMID: 16704732

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Normal blood cell subtypes

Project description:We used antibodies coupled to magnetic beads (MACS) to purify cell types out of whole blood from healthy donors (CD4+ T cells, CD8+ T cells, and B cells). We also profiled whole blood (collected in Pax tubes) and Peripheral Blood Mononuclear cells obtained by Ficoll-Paque based separation. RNA was extracted using Trizol, amplified linearly twice, labeled with Cy5 and co-hybridized with amplified Stratagene human reference (labeled with Cy3). A reference experiement design type is where all samples are compared to a common reference. Keywords: reference_design

2006-05-23 | GSE4889 | GEO

Normal blood cell subtypes

2006-05-23 | E-GEOD-4889 | biostudies-arrayexpress

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes and progenitors

Project description:Peripheral blood mononuclear cells (PBMCs) were isolated from fresh blood using Ficoll-Paque density gradient centrifugation. Single-cell suspensions were stained with different antibody cocktails designed to enrich for particular immune cell populations, which were then single cell sorted in 96-well plates. Single cell RNA-sequencing libraries were subsequently generated for 2422 single cells using Smart-Seq2 (Picelli et al., Nature Methods, 2014). Cells were sequenced at a depth of 1-2M reads/cell.

2017-04-21 | GSE94820 | GEO

Elevated acid ceramidase promotes acute myeloid leukemia blast survival through sphingolipid dysregulation and Mcl-1 upregulation

Project description:Gene expression of patient samples with acute myeloid leukemia (AML) were compared to normal controls to study dysregulated signalling pathways. Peripheral blood mononuclear cells (PBMCs) from primary AML patient samples were isolated using the Ficoll-Paque gradient separation method. RNA from CD34+ bone marrow cells of healthy donors were purchased from AllCells LLC (Alameda, CA; catalog number RNA-BM003C). Total RNA were harvested from patient samples using Trizol and subjected to microarray-based gene expression analysis.

2017-06-19 | GSE65409 | GEO

Immune cell subsets and their gene expression profiles from human PBMC isolated by Vacutainer Cell Preparation Tube and standard density gradient

2015-08-28 | GSE67321 | GEO

Immune cell subsets and their gene expression profiles from human PBMC isolated by Vacutainer Cell Preparation Tube and standard density gradient

Project description:High quality genetic material is an essential pre-requisite when analyzing gene expression using microarray technology. Peripheral blood mononuclear cells (PBMC) are frequently used for genomic analyses, but several factors can affect the integrity of nucleic acids prior to their extraction, including the methods of PBMC collection and isolation. In this study, we compared the Ficoll-Paque density gradient centrifugation and BD Vacutainer cell preparation tube (CPT) protocols to determine if either method offered a distinct advantage in preparation of PBMC-derived immune cell subsets for their use in gene expression analysis. We compared gene expression in PBMC and individual immune cell types from Ficoll and CPT isolation protocols using Affymetrix microarrays. PBMC from 3 healthy donors were isolated using Ficoll-Paque gradient or BD Vacutainer CPT methods. Subsequently, immune cell subsets were separated by positive selection from PBMC obtained by both methods. RNA was extracted from total PBMC isolated by both protocols and from their subsets, followed by analysis of gene expression using Affymetrix microarrays. Gene expression was compared between Ficoll and CPT samples for a given cell type.

2015-08-28 | E-GEOD-67321 | biostudies-arrayexpress

Unique RNA Expression Patterns in Serum Exosomes from Patients with Glioblastoma Multiforme

Project description:Comparative expression analysis of RNA isolated from microvesicles from serum from glioblastoma multiforme (GBM) patients and normal healthy individuals. Blood samples from 9 patients diagnosed with de-novo primary GBM were collected immediately prior to surgery. Blood from 7 normal healthy controls was collected from volunteers recruited at the MGH blood bank. From each sample, RNA was isolated from microvesicles isolated from 1 mL of serum, and the RNA was linearly amplified and labeled with Cy3. The amplified and labeled RNA was hybridized to 16 individual Agilent Arrays.

2011-12-01 | E-GEOD-24084 | biostudies-arrayexpress

Gene expression profiling of neutrophils from patients with cirrhosis and acute on chronic liver failure (ACLF)

Project description:Neutrophils were isolated (using Ficoll, Dextran and water to lyse the red cells) from whole blood of 5 healthy subjects, 5 patients with stable cirrhosis and 5 patients with ACLF. RNA was then extracted and amplified 100 ng of RNA per sample were then hybridized on ClarionS array (Affymetrix, Thermofischer scientific)

2021-02-24 | GSE142254 | GEO

Transcriptomic profiling in childhood H1N1/09 influenza reveals reduced expression of protein synthesis genes

Project description:In order to understand the immunopathogenesis of severe influenza H1N1/09, we compared the whole blood RNA transcriptome of children hospitalised with H1N1/09 infection with that of children hospitalised with RSV or bacterial infection Blood was collected into PAX gene tubes (PreAnalytiX). Total RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). Labeled cRNA was hybridized to Illumina Human HT-12 v3 Beadchips.

2013-09-05 | GSE42026 | GEO

Transcriptome profiling of purified red blood cells from Nxf1 mutant and control mice [Erythrocytes]

Project description:Purpose: Nxf1 is thought to be an essential nuclear exporter of messenger RNA (mRNA) in eukaryotic cells. Whether perturbations in the Nxf1 pathway affect mammalian physiology is not known. The aim of this study is to determine the impact of a Nxf1 mutation in the representation of mRNA transcripts in erythrocytes. Methods: Red blood cells were obtained from cardiac puncture, mixed with 100µl Aster Jandl citrate-based anticoagulant and subsequently diluted in 2 ml of phosphate buffer saline (PBS) with 2mM EDTA. This suspension was layered with 1.5 ml Ficoll-paque PLUS (GE Healthcare) and centrifuged at 400g for 30 minutes at room temperature with minimal acceleration and brake. The red blood cell containing pellet was washed twice with PBS 2mM EDTA and lysed for RNA extraction. The purity of each sample was checked by flow cytometry to assess the relative contamination of Ter199+ red blood cells with CD41+ platelets, CD45+ lymphocytes and DRAQ5+ (Thermo Fisher Scientific) nucleated cells. Red blood cell suspensions used for RNAseq were > 99.8% pure. RNA was extracted with Qiagen RNA extraction kit.

2020-03-04 | GSE141160 | GEO

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